Inferring Functional Pathways from Multi-Perturbation Data. - Nir Yosef; Alon Kaufman; Eytan Ruppin (ISMB (Supplement of Bioinformatics), 2006)

A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data. - Nir Yosef; Zohar Yakhini; Anya Tsalenko; Vessela N. Kristensen; Anne-Lise Børresen-Dale; Eytan Ruppin; Roded Sharan (Bioinform., 2007)

Cross-Species Analysis of Protein-protein Interaction Networks. - Nir Yosef; Eytan Ruppin; Roded Sharan (Protein-protein Interactions and Networks, 2008)

Improved network-based identification of protein orthologs. - Nir Yosef; Roded Sharan; William Stafford Noble (ECCB, 2008)

Network models of cellular response to perturbation - Nir Yosef (2009)

Prediction of Phenotype Information from Genotype Data. - Jens Gramm; Richard M. Karp; William S. Noble; Roded Sharan; Qianfei Wang; Nir Yosef (Commun. Inf. Syst., 2010)

Network-Free Inference of Knockout Effects in Yeast. - Tal Peleg; Nir Yosef; Eytan Ruppin; Roded Sharan (PLoS Comput. Biol., 2010)

FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data. - David DeTomaso; Nir Yosef (BMC Bioinform., 2016)

Offline Directed Steiner Network Problems on Dynamic Graphs. - Benjamin Weitz; Jimmy Wu; Nir Yosef (CoRR, 2016)

ImpulseDE: detection of differentially expressed genes in time series data using impulse models. - Jil Sander; Joachim L. Schultze; Nir Yosef (Bioinform., 2017)

A deep generative model for gene expression profiles from single-cell RNA sequencing. - Romain Lopez; Jeffrey Regier; Michael I. Jordan; Nir Yosef (CoRR, 2017)

Information Constraints on Auto-Encoding Variational Bayes. - Romain Lopez; Jeffrey Regier; Michael I. Jordan; Nir Yosef (NeurIPS, 2018)

A Deep Generative Model for Semi-Supervised Classification with Noisy Labels. - Maxime Langevin; Edouard Mehlman; Jeffrey Regier; Romain Lopez; Michael I. Jordan; Nir Yosef (CoRR, 2018)

Connectivity problems on heterogeneous graphs. - Jimmy Wu; Alex Khodaverdian; Benjamin Weitz; Nir Yosef (Algorithms Mol. Biol., 2019)

A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurements. - Romain Lopez; Achille Nazaret; Maxime Langevin; Jules Samaran; Jeffrey Regier; Michael I. Jordan; Nir Yosef (CoRR, 2019)

Decision-Making with Auto-Encoding Variational Bayes. - Romain Lopez; Pierre Boyeau; Nir Yosef; Michael I. Jordan; Jeffrey Regier (NeurIPS, 2020)

Interpretable factor models of single-cell RNA-seq via variational autoencoders. - Valentine Svensson; Adam Gayoso; Nir Yosef; Lior Pachter (Bioinform., 2020)

Identifying Systematic Variation at the Single-Cell Level by Leveraging Low-Resolution Population-Level Data. - Elior Rahmani; Michael I. Jordan; Nir Yosef (RECOMB, 2022)

AutoEval Done Right: Using Synthetic Data for Model Evaluation. - Pierre Boyeau; Anastasios N. Angelopoulos; Nir Yosef; Jitendra Malik; Michael I. Jordan (CoRR, 2024)

Tree Reconstruction Guarantees from CRISPR-Cas9 Lineage Tracing Data Using Neighbor-Joining. - Sebastian Prillo; Kevin An; Wilson Wu; Ivan Kristanto; Matthew G. Jones; Yun S. Song; Nir Yosef (RECOMB, 2025)